Contacts of the strand formed by residues 1473 - 1480 (chain B) in PDB entry 1XTB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR1473 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1053B ASP 4.4 1.7 - - - +
1056B LYS* 3.0 35.4 + - - +
1057B ASN* 3.5 14.0 + - - -
1403B CYS* 3.3 13.5 - - + +
1405B PHE* 3.9 12.3 - - + -
1432B THR* 3.4 28.9 + - + +
1435B LEU* 3.4 35.0 - - + -
1471B ARG 3.9 5.3 + - - +
1472B PRO* 1.3 82.3 - - - +
1474B ASN* 1.3 62.5 + - - +
1475B SER* 4.9 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1474 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1052B LEU* 4.6 8.3 - - + -
1053B ASP 3.6 4.0 - - - +
1054B TYR* 3.1 15.8 - - - +
1057B ASN* 2.8 30.4 + - - +
1319B LEU* 3.8 22.8 + - - +
1322B LEU* 3.8 11.6 - - - +
1326B TYR* 6.2 0.6 - - - -
1403B CYS 2.8 5.7 + - - +
1404B ASP* 2.9 29.7 + - - +
1405B PHE* 2.8 31.0 + - - +
1473B THR* 1.3 73.9 - - - +
1475B SER* 1.3 61.5 + - - +
1476B ILE* 4.0 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1475 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A LEU* 3.7 36.1 - - - +
1051B LEU 3.3 3.5 - - - +
1052B LEU* 3.8 0.5 - - - -
1053B ASP* 2.9 37.7 + - - +
1056B LYS* 4.3 2.6 + - - -
1405B PHE 3.4 4.3 - - - -
1428B PHE* 4.0 13.7 - - - -
1432B THR* 3.7 25.6 + - - +
1473B THR* 4.3 0.9 + - - -
1474B ASN* 1.3 72.5 - - - +
1476B ILE* 1.3 61.6 + - - +
1477B VAL* 3.9 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1476 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1050B ILE* 4.1 23.1 - - + -
1051B LEU 3.3 4.5 - - - +
1052B LEU* 3.7 23.8 - - + -
1319B LEU* 4.6 4.5 - - + -
1404B ASP* 4.3 9.4 - - - +
1405B PHE 2.7 13.8 + - - +
1406B LEU* 3.2 17.8 - - + +
1407B ILE 3.1 24.3 + - - +
1428B PHE* 4.4 0.2 - - - -
1474B ASN* 4.8 2.7 - - + +
1475B SER* 1.3 76.8 - - - +
1477B VAL* 1.3 61.0 + - - +
1478B PHE* 4.0 3.9 - - + -
1489B LEU* 4.3 17.3 - - + -
1492B MET* 3.8 20.6 - - + -
1493B TYR* 3.2 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1477 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A LEU* 3.8 25.1 - - + -
547A PHE* 3.5 21.2 - - + -
548A ILE* 4.4 10.5 - - + -
1050B ILE* 3.4 1.7 - - - -
1051B LEU* 2.6 40.7 + - + +
1407B ILE* 3.4 15.0 - - + +
1409B VAL* 3.6 27.1 - - + +
1428B PHE* 3.8 28.0 - - + -
1476B ILE* 1.3 77.7 - - - +
1478B PHE* 1.3 63.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1478 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A PHE* 4.6 0.9 - - - -
1049B HIS 3.1 10.5 - - - +
1050B ILE* 4.0 15.5 - - + -
1344B LEU* 4.6 10.8 - - + -
1406B LEU* 4.2 9.6 - - + -
1407B ILE* 3.2 21.1 + - - -
1408B PRO* 3.0 43.2 - - + +
1409B VAL* 2.7 34.7 + - - -
1476B ILE* 4.0 8.3 - - + -
1477B VAL* 1.3 78.3 - - - +
1479B THR* 1.3 58.8 + - - +
1480B LYS 3.7 13.9 - - - -
1481B LEU* 3.7 24.2 - - + -
1485B ILE* 3.9 13.2 - - + -
1489B LEU* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1479 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A PHE* 4.9 1.2 - - - -
551A GLN* 2.6 37.2 + - - +
554A ALA* 4.3 4.9 - - + -
556A ILE* 3.8 21.5 - - + -
1048B GLY* 3.8 8.5 - - - -
1049B HIS* 2.9 28.4 + - - +
1409B VAL* 3.6 9.1 - - - +
1410B GLN* 2.8 49.2 + - - +
1478B PHE* 1.3 71.0 - - - +
1480B LYS* 1.3 59.9 + - - +
1485B ILE* 5.8 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1480 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A ILE* 3.5 20.1 - - + +
1173B TYR* 4.4 3.2 + - - -
1408B PRO* 4.0 6.7 - - - -
1410B GLN* 3.6 33.5 - - + +
1411B THR 4.3 14.1 + - - -
1412B GLN* 3.4 35.3 + - - +
1478B PHE* 3.3 6.8 + - - -
1479B THR* 1.3 81.0 - - - +
1481B LEU* 1.3 62.8 + - - +
1482B THR* 3.1 18.8 + - + +
1485B ILE* 3.3 24.5 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il